Schema for xenoRefSeqAli
  Database: speTri2    Primary Table: xenoRefSeqAli    Row Count: 446,239   Data last updated: 2020-08-20
Format description: Summary info about a patSpace alignment
On download server: MariaDB table dump directory
fieldexampleSQL type info description
bin 585smallint(5) unsigned range Indexing field to speed chromosome range queries.
matches 557int(10) unsigned range Number of bases that match that aren't repeats
misMatches 115int(10) unsigned range Number of bases that don't match
repMatches 0int(10) unsigned range Number of bases that match but are part of repeats
nCount 0int(10) unsigned range Number of 'N' bases
qNumInsert 0int(10) unsigned range Number of inserts in query
qBaseInsert 0int(10) unsigned range Number of bases inserted in query
tNumInsert 3int(10) unsigned range Number of inserts in target
tBaseInsert 9229int(10) unsigned range Number of bases inserted in target
strand ++char(2) values + or - for strand. First character query, second target (optional)
qName NM_001171014varchar(255) values Query sequence name
qSize 1775int(10) unsigned range Query sequence size
qStart 887int(10) unsigned range Alignment start position in query
qEnd 1559int(10) unsigned range Alignment end position in query
tName AGTP01130780varchar(255) values Target sequence name
tSize 61863int(10) unsigned range Target sequence size
tStart 1901int(10) unsigned range Alignment start position in target
tEnd 11802int(10) unsigned range Alignment end position in target
blockCount 4int(10) unsigned range Number of blocks in alignment
blockSizes 138,85,220,229,longblob   Size of each block
qStarts 887,1025,1110,1330,longblob   Start of each block in query.
tStarts 1901,3225,4567,11573,longblob   Start of each block in target.

Connected Tables and Joining Fields
        hgFixed.gbCdnaInfo.acc (via xenoRefSeqAli.qName)
      hgFixed.gbMiscDiff.acc (via xenoRefSeqAli.qName)
      hgFixed.gbSeq.acc (via xenoRefSeqAli.qName)
      hgFixed.gbWarn.acc (via xenoRefSeqAli.qName)
      hgFixed.imageClone.acc (via xenoRefSeqAli.qName)
      speTri2.all_est.qName (via xenoRefSeqAli.qName)
      speTri2.all_mrna.qName (via xenoRefSeqAli.qName)
      speTri2.xenoRefFlat.name (via xenoRefSeqAli.qName)
      speTri2.xenoRefGene.name (via xenoRefSeqAli.qName)

Sample Rows
 
binmatchesmisMatchesrepMatchesnCountqNumInsertqBaseInserttNumInserttBaseInsertstrandqNameqSizeqStartqEndtNametSizetStarttEndblockCountblockSizesqStartstStarts
585557115000039229++NM_00117101417758871559AGTP01130780618631901118024138,85,220,229,887,1025,1110,1330,1901,3225,4567,11573,
5855131100011239241++NM_00102986718889021537AGTP01130780618631902117664137,85,209,192,902,1039,1124,1345,1902,3225,4567,11574,
585506121001839237++NM_17288133589001535AGTP01130780618631902117664137,73,226,191,900,1045,1118,1344,1902,3233,4563,11575,
585519120000049229++NM_15331418199021541AGTP01130780618631902117705137,79,225,2,196,902,1039,1118,1343,1345,1902,3225,4561,4805,11574,
585554770013449263++NM_00117214116268821547AGTP01130780618631902117965136,5,43,224,223,882,1018,1023,1100,1324,1902,2129,3229,4563,11573,
58557689000039229++NM_00117214316318841549AGTP01130780618631902117964137,81,223,224,884,1021,1102,1325,1902,3225,4563,11572,
673151622200112791940393++NM_025264220512018JH39331812730293115691881161131920144,136,207,199,78,58,83,72,113,109,160,144,5,14,7,10,66,14,47,72,1,145,281,492,691,769,827,911,984,1097,1206,1387,1602,1608,1627,1647,1684,1878,1899,1946,11569188,11576823,11578226,11578440,11579594,11581563,11587198,11594214,11594761,11604041,11610313,11610494,11610895,11610902,11 ...
731169840052151355232++NM_0062921534441512JH393338100155457526128090971515,102,85,33,78,45,4,64,92,203,240,97,33,34,128,44,66,168,318,483,561,606,610,674,766,969,1209,1315,1348,1384,752612,752633,759675,764197,771741,771822,771876,775898,786756,805574,807236,808798,808895,808934,808969,
76961985001312261++NM_00104615615405712JH3932814149396424133196241361613352,298,54,5,357,658,24133196,24135809,24136107,
585490145003300351602++NM_13389418949031838AGTP01130780618631902541394137,214,236,48,903,1120,1341,1790,1902,4562,11569,54091,

Note: all start coordinates in our database are 0-based, not 1-based. See explanation here.